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WASHINGTON — In a move that will sadden and anger many submariners, the Navy has concluded the cost to repair the nuclear attack submarine Miami, severely damaged last year by an arsonist, is more than it can afford in an era where repair and maintenance funds are being slashed by mandated budget cuts.

“The decision to inactivate Miami is a difficult one, taken after hard analysis and not made lightly,” Rear Adm. Rick Breckenridge, the Navy’s director of undersea warfare at the Pentagon, said in a statement released Tuesday evening.

“We will lose the five deployments that Miami would have provided over the remaining ten years of her planned service life, but in exchange for avoiding the cost of repairs, we will open up funds to support other vital maintenance efforts, improving the wholeness and readiness of the fleet.”

The Navy last year estimated that repairs to the Los Angeles-class submarine would cost at least $450 million, and at least $94 million has been spent to plan the repair work.

But after what a Navy official termed a “comprehensive damage assessment” conducted over the past year, the estimated repair costs have risen dramatically.

“The increased cost estimate and scope means that without $390 million in additional funding in fiscal 2014, funding the repairs would require cancellation of dozens of remaining availabilities on surface ships and submarines,” Breckenridge said in the statement.

He noted that the cost would compound pressures from sequestration in 2014. “The Navy and the nation simply cannot afford to weaken other fleet readiness in the way that would be required to afford repairs to Miami,” Breckenridge said.

A key factor in the heightened cost estimate, the Navy official said, was the effect of “environmentally-assisted cracking” in the steel piping and fasteners used in the air, hydraulic and cooling water systems aboard the submarine, meaning much more equipment would have to be replaced than previously thought.

The official added that a review of other recent repair efforts on submarines suffering from major damage “revealed that planned contingency funds were insufficient.”

The Miami was devastated by a fire that broke out late in the work day on May 23, 2012, while the submarine was in drydock at Portsmouth Naval Shipyard in Kittery, Maine. Casey James Fury, 24, a civilian painter and sand blaster at the shipyard, was arrested after a three-week investigation and charged with arson. On Nov. 8 he pleaded guilty to the May 23 fire, and to a smaller fire set outside the submarine on June 16. He was sentenced on March 14 to more than 17 years in federal prison.

He set the May 23 fire, he told authorities, because he was having an anxiety attack, wanted to leave work and had already used up his sick leave.

The blaze burned for about 12 hours inside the submarine, which was only a few weeks into a planned 20-month overhaul. Fire teams from as far away as Boston and Connecticut battled intense fires throughout the night and into the next morning. The conflagration heavily damaged or destroyed the submarine's control room, combat systems and torpedo room.

Navy officials have repeatedly said the ship’s nuclear reactor was not threatened by the inferno. But temperatures inside the forward hull reached extreme levels and the lower portions of the bow section were flooded by firefighters.

Although many observers thought the damage would be fatal to the submarine, the Navy was determined to repair the ship. Privately, officials declared their resolve not to let an arsonist destroy a sophisticated and powerful warship.

After initial repair cost estimates were revised upward, the decision to repair the submarine was announced on Aug. 22 in a statement from the Naval Sea Systems Command (NAVSEA).

“The Navy’s revised cost estimate to restore USS Miami (SSN 755) is approximately $450 million, with an estimated date of completion for the repairs of April 30, 2015,” NAVSEA said in the Aug. 22 statement. “The estimate includes 10 percent variability due to the unique nature of the repair and the cost impacts of shifting the planned maintenance availabilities of other ships and submarines.

“The Navy is committed to delivering the submarine back to the fleet with no operational limitations. Once returned to service, Miami will serve for an additional 10 years with five planned full-length deployments, ready to respond to any combatant commander tasking,” the Aug. 22 statement concluded.

Built at the General Dynamics Electric Boat shipyard in Groton, Conn., the Miami was commissioned in June 1990 and had been expected to serve for 30 years.

While statistics haven’t been verified, the decision to scrap the submarine means the Miami could become the first warship — and submarine or nuclear-powered ship — to be lost while in the hands of a U.S. naval shipyard since the Civil War. A handful of ships have been lost since, but all those appear to have been at a commercial yard or pier.